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- PDB-4re1: Crystal structure of human TEAD1 and disulfide-engineered YAP -

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Basic information

Entry
Database: PDB / ID: 4re1
TitleCrystal structure of human TEAD1 and disulfide-engineered YAP
Components
  • Transcriptional enhancer factor TEF-1
  • Yorkie homolog
KeywordsTRANSCRIPTION/PROTEIN BINDING / immunoglobulin-like fold / Transcription regulation / DNA-binding / protein-protein interaction / phosphoprotein / nucleus / TRANSCRIPTION-PROTEIN BINDING complex
Function / homology
Function and homology information


enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / contact inhibition / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / bud elongation involved in lung branching ...enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / contact inhibition / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / bud elongation involved in lung branching / polarized epithelial cell differentiation / notochord development / negative regulation of cilium assembly / lung epithelial cell differentiation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / heart process / trophectodermal cell differentiation / paraxial mesoderm development / hippo signaling / regulation of stem cell proliferation / tissue homeostasis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / Formation of axial mesoderm / negative regulation of stem cell differentiation / embryonic heart tube morphogenesis / female germ cell nucleus / Signaling by Hippo / proline-rich region binding / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of epithelial cell differentiation / organ growth / positive regulation of stem cell population maintenance / interleukin-6-mediated signaling pathway / negative regulation of fat cell differentiation / positive regulation of Notch signaling pathway / RUNX2 regulates osteoblast differentiation / Zygotic genome activation (ZGA) / progesterone receptor signaling pathway / somatic stem cell population maintenance / regulation of neurogenesis / canonical Wnt signaling pathway / vasculogenesis / embryonic organ development / positive regulation of osteoblast differentiation / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / Nuclear signaling by ERBB4 / keratinocyte differentiation / positive regulation of cardiac muscle cell proliferation / epithelial cell proliferation / response to progesterone / positive regulation of epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / wound healing / cell morphogenesis / cellular response to gamma radiation / positive regulation of miRNA transcription / positive regulation of protein localization to nucleus / transcription corepressor activity / cell-cell junction / sequence-specific double-stranded DNA binding / positive regulation of canonical Wnt signaling pathway / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / protein-containing complex assembly / DNA-binding transcription factor binding / cell population proliferation / transcription regulator complex / transcription coactivator activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / DNA damage response / chromatin binding / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Virus Scaffolding Protein; Chain A / Virus Scaffolding Protein; Chain A - #10 / Coagulation Factor XIII; Chain A, domain 1 - #80 / TEA/ATTS domain / Transcriptional enhancer factor, metazoa / TEA/ATTS domain superfamily / TEA/ATTS domain / TEA domain signature. / TEA domain profile. / TEA domain ...Virus Scaffolding Protein; Chain A / Virus Scaffolding Protein; Chain A - #10 / Coagulation Factor XIII; Chain A, domain 1 - #80 / TEA/ATTS domain / Transcriptional enhancer factor, metazoa / TEA/ATTS domain superfamily / TEA/ATTS domain / TEA domain signature. / TEA domain profile. / TEA domain / YAP binding domain / YAP binding domain / Coagulation Factor XIII; Chain A, domain 1 / Other non-globular / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Distorted Sandwich / Special / Mainly Beta
Similarity search - Domain/homology
Transcriptional enhancer factor TEF-1 / Transcriptional coactivator YAP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsXu, Z. / Zhou, Z.
CitationJournal: Faseb J. / Year: 2015
Title: Targeting Hippo pathway by specific interruption of YAP-TEAD interaction using cyclic YAP-like peptides.
Authors: Zhou, Z. / Hu, T. / Xu, Z. / Lin, Z. / Zhang, Z. / Feng, T. / Zhu, L. / Rong, Y. / Shen, H. / Luk, J.M. / Zhang, X. / Qin, N.
History
DepositionSep 21, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional enhancer factor TEF-1
B: Transcriptional enhancer factor TEF-1
C: Yorkie homolog
D: Yorkie homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0095
Polymers82,9744
Non-polymers351
Water1,71195
1
A: Transcriptional enhancer factor TEF-1
D: Yorkie homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5223
Polymers41,4872
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-33 kcal/mol
Surface area12300 Å2
MethodPISA
2
B: Transcriptional enhancer factor TEF-1
C: Yorkie homolog


Theoretical massNumber of molelcules
Total (without water)41,4872
Polymers41,4872
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-24 kcal/mol
Surface area12180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.250, 105.030, 164.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcriptional enhancer factor TEF-1 / NTEF-1 / Protein GT-IIC / TEA domain family member 1 / TEAD-1 / Transcription factor 13 / TCF-13


Mass: 25509.078 Da / Num. of mol.: 2 / Fragment: YAP BINDING DOMAIN (UNP RESIDUES 209-426)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD1, TCF13, TEF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P28347
#2: Protein Yorkie homolog / 65 kDa Yes-associated protein / YAP65


Mass: 15977.824 Da / Num. of mol.: 2 / Fragment: TEAD BINDING DOMAIN (UNP RESIDUES 50-171) / Mutation: R87C, D93A, F96C, E100R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YAP1, YAP65 / Production host: Escherichia coli (E. coli) / References: UniProt: P46937
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate, 1.8M sodium formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→26.57 Å / Num. obs: 38411 / % possible obs: 96.8 % / Rmerge(I) obs: 0.08
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3532 / % possible all: 98.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KYS

3kys


Resolution: 2.2→26.57 Å / SU ML: 0.29 / σ(F): 1.33 / Phase error: 30.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2482 1905 4.98 %RANDOM
Rwork0.2119 ---
obs0.2137 38275 95.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→26.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3895 0 1 95 3991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094052
X-RAY DIFFRACTIONf_angle_d1.1145498
X-RAY DIFFRACTIONf_dihedral_angle_d14.4121441
X-RAY DIFFRACTIONf_chiral_restr0.046622
X-RAY DIFFRACTIONf_plane_restr0.006712
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.2550.35991350.311257497
2.255-2.31590.35151310.289259697
2.3159-2.3840.31761290.267259597
2.384-2.46090.33491360.2678260897
2.4609-2.54880.31761260.2508255497
2.5488-2.65080.26471340.2472259196
2.6508-2.77130.32081250.2535260096
2.7713-2.91730.28191470.2509258596
2.9173-3.09980.31271280.2495257696
3.0998-3.33870.30891360.2366260096
3.3387-3.67390.24761550.2049260196
3.6739-4.20370.21551510.1817259796
4.2037-5.28940.17251390.1553262594
5.2894-26.57190.21741330.2013266891

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